[MMTK] Bug (?) in reading/writing PDBs

Konrad Hinsen hinsen at cnrs-orleans.fr
Sun Feb 1 17:18:43 CET 2004


On 31.01.2004, at 14:55, Urban Hafner wrote:

> The PDB file is 1aru from PDB. But this doesn't just happen with this 
> file but
> with every PDB that ends with Proline. If you compare the two pdbs you 
> see this
> difference:
...

> The difference seems to be between OXT in the original file and O1 and 
> O2
> in the second one.
>
> So is this a bug in MMTK or in Scientific Python and is there 
> something I
> can do about it?
>
The bug is in the database definition file for the peptide group of 
C-terminal proline, which has O1 and O2 instead of the PDB standard 
names O and OXT. Just put the attached files into MMTK/Database/Groups 
and your script works fine.

Konrad.
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